PyPhyloGenomicsTools to work in phylogenomics, from NSG group http://nymphalidae.utu.fiPyPhyloGenomics
===============
A package to work on Phylogenomics.
[[In development.]]
Developers
----------
- Carlos Peña (email: carlos.pena@utu.fi)
- Victor Solis
- Pavel Matos
- Chris Wheat
Installing PyPhyloGenomics
--------------------------
PyPhyloGenomics has been developed in Python v2.7. The installer of
PyPhyloGenomics will try to download and install all its dependencies as
well. To install PyPhyloGenomics use setup.py:
python setup.py build
python setup.py install
If it fails you can install the dependencies manually:
Install dependencies:
---------------------
requests:
The package requests from here. Or try:
sudo apt-get install python-requests
Parallel Python (pp):
If you are using Ubuntu Linux or related:
sudo apt-get install python-pp
Otherwise, download the source code and install pp:
unzip pp-1.6.4.zip
cd pp-1.6.4
python setup.py install
BioPython:
Download and install from here. Or:
sudo apt-get install python-biopython
BeatutifulSoup
Download and install from here. Or:
sudo apt-get install python-bs4
MUSCLE
It is necessary that you install MUSCLE so that PyPhyloGenomics can use
it to align sequences. Download and install from here.
If you are using Windows you can download the executable file
muscle3.8.31_i86win32.exe and save it in your Python folder (C:27) as
muscle.exe.
BLAST
Download and install the BLAST+ executables from the NCBI website. Or
try:
sudo apt-get install ncbi-blast+
fastx-toolkit
Download and install from here. Or:
sudo apt-get install fastx-toolkit
Reading PyPhyloGenomics' documentation:
---------------------------------------
Read the online documentation here:
http://carlosp420.github.io/PyPhyloGenomics/
Or, after installling do the following:
cd doc
make html
Then open the file _build/html/index.html in your web-browser.
Reproduce our analysis:
-----------------------
You can reproduce all the steps detailed in our [Getting started with
PyPhylogenomics] guide. Just use the command line in the same folder as
the Makefile and type make ???http://carlosp420.github.com/PyPhyloGenomics/Carlos Pena, Victor Solis, Pavel Matos, Chris Wheat3c1bd1e35fdee1f51d0654c7c7d97eab9945b1b70.3.7